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  1. Predicting protein structure from amino acid sequence is a prominent problem in computational biology. The long range interactions (or non-local interactions) are known as the main source of complexity for pro...

    Authors: Yuzhen Guo, Fengying Tao, Zikai Wu and Yong Wang
    Citation: BMC Systems Biology 2017 11(Suppl 4):93

    This article is part of a Supplement: Volume 11 Supplement 4

  2. Influenza A virus is prone to mutation and susceptible to human beings and spread in the crowds when affected by the external environment or other factors. It is very necessary to forecast influenza A pandemic...

    Authors: Jie Gao, Kang Wang, Tao Ding and Shanshan Zhu
    Citation: BMC Systems Biology 2017 11(Suppl 4):85

    This article is part of a Supplement: Volume 11 Supplement 4

  3. The Notch family of proteins plays a vital role in determining cell fates, such as proliferation, differentiation, and apoptosis. It has been shown that Notch1 and its ligands, Dll1 and Jag1, are overexpressed...

    Authors: Xiaofei Shi and Ruiqi Wang
    Citation: BMC Systems Biology 2017 11(Suppl 4):84

    This article is part of a Supplement: Volume 11 Supplement 4

  4. The Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNE) represents one of the most effective tools to reconstruct gene regulatory networks from large-scale molecular profile datasets. Howev...

    Authors: Jing He, Zhou Zhou, Michael Reed and Andrea Califano
    Citation: BMC Systems Biology 2017 11(Suppl 4):83

    This article is part of a Supplement: Volume 11 Supplement 4

  5. The boundary formation in the Drosophila large intestine is widely studied as an important biological problem. It has been shown that the Delta-Notch signaling pathway plays an essential role in the formation of ...

    Authors: Fei Liu, Deshun Sun, Ryutaro Murakami and Hiroshi Matsuno
    Citation: BMC Systems Biology 2017 11(Suppl 4):80

    This article is part of a Supplement: Volume 11 Supplement 4

  6. The human phenome has been widely used with a variety of genomic data sources in the inference of disease genes. However, most existing methods thus far derive phenotype similarity based on the analysis of bio...

    Authors: Mingxin Gan, Wenran Li, Wanwen Zeng, Xiaojian Wang and Rui Jiang
    Citation: BMC Systems Biology 2017 11(Suppl 4):76

    This article is part of a Supplement: Volume 11 Supplement 4

  7. High-throughput experimental techniques have been dramatically improved and widely applied in the past decades. However, biological interpretation of the high-throughput experimental results, such as different...

    Authors: Duanchen Sun, Yinliang Liu, Xiang-Sun Zhang and Ling-Yun Wu
    Citation: BMC Systems Biology 2017 11(Suppl 4):75

    This article is part of a Supplement: Volume 11 Supplement 4

  8. Acute myelogenous leukemia (AML) progresses uniquely in each patient. However, patients are typically treated with the same types of chemotherapy, despite biological differences that lead to differential respo...

    Authors: Joyatee M. Sarker, Serena M. Pearce, Robert P. Nelson Jr., Tamara L. Kinzer-Ursem, David M. Umulis and Ann E. Rundell
    Citation: BMC Systems Biology 2017 11:78
  9. The high-dose hook effect (also called prozone effect) refers to the observation that if a multivalent protein acts as a linker between two parts of a protein complex, then increasing the amount of linker prot...

    Authors: Ranjita Dutta Roy, Christian Rosenmund and Melanie I. Stefan
    Citation: BMC Systems Biology 2017 11:74
  10. High-throughput assays are widely used in biological research to select potential targets. One single high-throughput experiment can efficiently study a large number of candidates simultaneously, but is subjec...

    Authors: Wenfei Zhang, Ying Liu, Mindy Zhang, Cheng Zhu and Yuefeng Lu
    Citation: BMC Systems Biology 2017 11:73
  11. Signal transduction pathways are important cellular processes to maintain the cell’s integrity. Their imbalance can cause severe pathologies. As signal transduction pathways feature complex regulations, they f...

    Authors: Leonie Amstein, Jörg Ackermann, Jennifer Scheidel, Simone Fulda, Ivan Dikic and Ina Koch
    Citation: BMC Systems Biology 2017 11:72
  12. A unique combination of mechanical, physiochemical and biological forces influences granulation during processes of anaerobic digestion. Understanding this process requires a systems biology approach due to th...

    Authors: Anna Doloman, Honey Varghese, Charles D. Miller and Nicholas S. Flann
    Citation: BMC Systems Biology 2017 11:69
  13. Triple-negative breast cancer lacks estrogen, progesterone, and HER2 receptors and is thus not possible to treat with targeted therapies for these receptors. Therefore, a greater understanding of triple-negati...

    Authors: Kerri-Ann Norton, Travis Wallace, Niranjan B. Pandey and Aleksander S. Popel
    Citation: BMC Systems Biology 2017 11:68
  14. Large sets of protein-protein interaction data coming either from biological experiments or predictive methods are available and can be combined to construct networks from which information about various cell ...

    Authors: Annie Glatigny, Philippe Gambette, Alexa Bourand-Plantefol, Geneviève Dujardin and Marie-Hélène Mucchielli-Giorgi
    Citation: BMC Systems Biology 2017 11:67
  15. Nannochloropsis salina (= Eustigmatophyceae) is a marine microalga which has become a biotechnological target because of its high capacity to produce polyunsaturated fatty acids and tr...

    Authors: Nicolás Loira, Sebastian Mendoza, María Paz Cortés, Natalia Rojas, Dante Travisany, Alex Di Genova, Natalia Gajardo, Nicole Ehrenfeld and Alejandro Maass
    Citation: BMC Systems Biology 2017 11:66
  16. α2-adrenoceptors are important regulators of vascular tone and blood pressure. Regulation of cell proliferation is a less well investigated consequence of α2-adrenoceptor activation. We have previously shown that...

    Authors: Anna Huhtinen, Vesa Hongisto, Asta Laiho, Eliisa Löyttyniemi, Dirk Pijnenburg and Mika Scheinin
    Citation: BMC Systems Biology 2017 11:65
  17. Obesity is frequently linked to insulin resistance, high insulin levels, chronic inflammation, and alterations in the behaviour of CD4+ T cells. Despite the biomedical importance of this condition, the system-...

    Authors: Mariana E. Martinez-Sanchez, Marcia Hiriart and Elena R. Alvarez-Buylla
    Citation: BMC Systems Biology 2017 11:64
  18. In quantitative biology, mathematical models are used to describe and analyze biological processes. The parameters of these models are usually unknown and need to be estimated from experimental data using stat...

    Authors: Benjamin Ballnus, Sabine Hug, Kathrin Hatz, Linus Görlitz, Jan Hasenauer and Fabian J. Theis
    Citation: BMC Systems Biology 2017 11:63
  19. Co-expression has been widely used to identify novel regulatory relationships using high throughput measurements, such as microarray and RNA-seq data. Evaluation studies on co-expression network analysis metho...

    Authors: Wenbin Guo, Cristiane P. G. Calixto, Nikoleta Tzioutziou, Ping Lin, Robbie Waugh, John W. S. Brown and Runxuan Zhang
    Citation: BMC Systems Biology 2017 11:62
  20. Finding gene-disease and disease-disease associations play important roles in the biomedical area and many prioritization methods have been proposed for this goal. Among them, approaches based on a heterogeneo...

    Authors: Duc-Hau Le and Van-Huy Pham
    Citation: BMC Systems Biology 2017 11:61
  21. Type 2 diabetes is one of the leading non-infectious diseases worldwide and closely relates to excess adipose tissue accumulation as seen in obesity. Specifically, hypertrophic expansion of adipose tissues is ...

    Authors: Thierry Chénard, Frédéric Guénard, Marie-Claude Vohl, André Carpentier, André Tchernof and Rafael J. Najmanovich
    Citation: BMC Systems Biology 2017 11:60
  22. The yeast AMPK/SNF1 pathway is best known for its role in glucose de/repression. When glucose becomes limited, the Snf1 kinase is activated and phosphorylates the transcriptional repressor Mig1, which is then ...

    Authors: Niek Welkenhuysen, Johannes Borgqvist, Mattias Backman, Loubna Bendrioua, Mattias Goksör, Caroline B Adiels, Marija Cvijovic and Stefan Hohmann
    Citation: BMC Systems Biology 2017 11:59
  23. The increase in glycerol obtained as a byproduct of biodiesel has encouraged the production of new industrial products, such as 1,3-propanediol (PDO), using biotechnological transformation via bacteria like Clost...

    Authors: Luis Miguel Serrano-Bermúdez, Andrés Fernando González Barrios, Costas D. Maranas and Dolly Montoya
    Citation: BMC Systems Biology 2017 11:58
  24. Iron is an essential element of most living organisms but is a dangerous substance when poorly liganded in solution. The hormone hepcidin regulates the export of iron from tissues to the plasma contributing to...

    Authors: Jignesh H. Parmar, Grey Davis, Hope Shevchuk and Pedro Mendes
    Citation: BMC Systems Biology 2017 11:57
  25. The human gut contains approximately 1014 bacteria, belonging to hundreds of different species. Together, these microbial species form a complex food web that can break down nutrient sources that our own digestiv...

    Authors: Milan J. A. van Hoek and Roeland M. H. Merks
    Citation: BMC Systems Biology 2017 11:56
  26. Mechanical and biophysical properties of the cellular microenvironment regulate cell fate decisions. Mesenchymal stem cell (MSC) fate is influenced by past mechanical dosing (memory), but the mechanisms underl...

    Authors: Tao Peng, Linan Liu, Adam L MacLean, Chi Wut Wong, Weian Zhao and Qing Nie
    Citation: BMC Systems Biology 2017 11:55
  27. Kinetic models of biochemical systems usually consist of ordinary differential equations that have many unknown parameters. Some of these parameters are often practically unidentifiable, that is, their values ...

    Authors: Attila Gábor, Alejandro F. Villaverde and Julio R. Banga
    Citation: BMC Systems Biology 2017 11:54
  28. With the advance of experimental techniques such as time-lapse fluorescence microscopy, the availability of single-cell trajectory data has vastly increased, and so has the demand for computational methods sui...

    Authors: Irena Kuzmanovska, Andreas Milias-Argeitis, Jan Mikelson, Christoph Zechner and Mustafa Khammash
    Citation: BMC Systems Biology 2017 11:52
  29. The leading edge of the global problem of antibiotic resistance necessitates novel therapeutic strategies. This study develops a novel systems biology driven approach for killing antibiotic resistant pathogens...

    Authors: Deepanwita Banerjee, Dharmeshkumar Parmar, Nivedita Bhattacharya, Avinash D. Ghanate, Venkateswarlu Panchagnula and Anu Raghunathan
    Citation: BMC Systems Biology 2017 11:51
  30. Essential reactions are vital components of cellular networks. They are the foundations of synthetic biology and are potential candidate targets for antimetabolic drug design. Especially if a single reaction i...

    Authors: Abraham A. Labena, Yuan-Nong Ye, Chuan Dong, Fa-Z Zhang and Feng-Biao Guo
    Citation: BMC Systems Biology 2017 11:50
  31. Microbial production of nitrogen containing compounds requires a high uptake flux and assimilation of the N-source (commonly ammonium), which is generally coupled with ATP consumption and negatively influences...

    Authors: Hugo F. Cueto-Rojas, Nicholas Milne, Ward van Helmond, Mervin M. Pieterse, Antonius J. A. van Maris, Jean-Marc Daran and S. Aljoscha Wahl
    Citation: BMC Systems Biology 2017 11:49
  32. Transforming growth factor β (TGF-β) signalling regulates the development of embryos and tissue homeostasis in adults. In conjunction with other oncogenic changes, long-term perturbation of TGF-β signalling is as...

    Authors: Shabnam Khatibi, Hong-Jian Zhu, John Wagner, Chin Wee Tan, Jonathan H. Manton and Antony W. Burgess
    Citation: BMC Systems Biology 2017 11:48
  33. Weighted Gene Co-expression Network Analysis (WGCNA) is a widely used R software package for the generation of gene co-expression networks (GCN). WGCNA generates both a GCN and a derived partitioning of cluste...

    Authors: Juan A. Botía, Jana Vandrovcova, Paola Forabosco, Sebastian Guelfi, Karishma D’Sa, John Hardy, Cathryn M. Lewis, Mina Ryten and Michael E. Weale
    Citation: BMC Systems Biology 2017 11:47
  34. Cancer reversion, converting the phenotypes of a cancer cell into those of a normal cell, has been sporadically observed throughout history. However, no systematic analysis has been attempted so far.

    Authors: Yunseong Kim, Sea Choi, Dongkwan Shin and Kwang-Hyun Cho
    Citation: BMC Systems Biology 2017 11:45
  35. Time-lapse microscopy is an essential tool for capturing and correlating bacterial morphology and gene expression dynamics at single-cell resolution. However state-of-the-art computational methods are limited ...

    Authors: Athanasios D. Balomenos, Panagiotis Tsakanikas, Zafiro Aspridou, Anastasia P. Tampakaki, Konstantinos P. Koutsoumanis and Elias S. Manolakos
    Citation: BMC Systems Biology 2017 11:43
  36. Early afterdepolarizations (EADs) are pathological voltage oscillations during the repolarization phase of cardiac action potentials (APs). EADs are caused by drugs, oxidative stress or ion channel disease, an...

    Authors: Philipp Kügler, M.A.K. Bulelzai and André H. Erhardt
    Citation: BMC Systems Biology 2017 11:42
  37. Parameter optimisation is a critical step in the construction of computational biology models. In eye movement research, computational models are increasingly important to understanding the mechanistic basis o...

    Authors: Eleftherios Avramidis and Ozgur E. Akman
    Citation: BMC Systems Biology 2017 11:40
  38. Directed cell migration can be driven by a range of external stimuli, such as spatial gradients of: chemical signals (chemotaxis); adhesion sites (haptotaxis); or temperature (thermotaxis). Continuum models of...

    Authors: Matthew J. Simpson, Kai-Yin Lo and Yung-Shin Sun
    Citation: BMC Systems Biology 2017 11:39
  39. Protein secretion is one of the most important processes in eukaryotes. It is based on a highly complex machinery involving numerous proteins in several cellular compartments. The elucidation of the cell biolo...

    Authors: Anne Mathilde Lund, Christian Schrøder Kaas, Julian Brandl, Lasse Ebdrup Pedersen, Helene Faustrup Kildegaard, Claus Kristensen and Mikael Rørdam Andersen
    Citation: BMC Systems Biology 2017 11:37
  40. Cellular senescence irreversibly arrests growth of human diploid cells. In addition, recent studies have indicated that senescence is a multi-step evolving process related to important complex biological proce...

    Authors: Chihyun Park, So Jeong Yun, Sung Jin Ryu, Soyoung Lee, Young-Sam Lee, Youngmi Yoon and Sang Chul Park
    Citation: BMC Systems Biology 2017 11:36
  41. An orphan disease is any disease that affects a small percentage of the population. Orphan diseases are a great burden to patients and society, and most of them are genetic in origin. Unfortunately, our curren...

    Authors: Xiaoxia Liu, Zhihao Yang, Hongfei Lin, Michael Simmons and Zhiyong Lu
    Citation: BMC Systems Biology 2017 11(Suppl 3):23

    This article is part of a Supplement: Volume 11 Supplement 3

  42. Most disease-associated variants identified by genome-wide association studies (GWAS) exist in noncoding regions. In spite of the common agreement that such variants may disrupt biological functions of their h...

    Authors: Qiao Liu, Mingxin Gan and Rui Jiang
    Citation: BMC Systems Biology 2017 11(Suppl 2):7

    This article is part of a Supplement: Volume 11 Supplement 2

  43. Bruton tyrosine kinase (Btk) plays an important role in B-cell development, differentiation, and signaling. It is also found be in involved in male immunodeficiency disease such as X-linked agammaglobulinemia ...

    Authors: Pavithra K. Balasubramanian, Anand Balupuri, Hee-Young Kang and Seung Joo Cho
    Citation: BMC Systems Biology 2017 11(Suppl 2):6

    This article is part of a Supplement: Volume 11 Supplement 2